Explicit time integration algorithm for fully flexible cell simulation

외연적 적분 기법을 적용한 Fully Flexible Cell 분자 동영학 시뮬레이션

Fully flexible cell preserves Hamiltonian in structure, so the symplectic time integrator is applied to the equations of motion. Primarily, generalized leapfrog time integration (GLF) is applicable, but the equations of motion by GLF have some of implicit formulas. The implicit formulas give rise to a complicate calculation for coding and need an iteration process. In this paper, the time integration formulas are obtained for the fully flexible cell molecular dynamics simulation by using the splitting time integration. It separates flexible cell Hamiltonian into terms corresponding to each of Hamiltonian term, so the simple and completely explicit recursion formula was obtained. The explicit formulas are easy to implementation for coding and may be reduced the integration time because they are not need iteration process. We are going to compare the resulting splitting time integration with the implicit generalized leapfrog time integration.